Basal forebrain cholinergic neuron (BFCN) degeneration is an indicator of Down syndrome (DS) and Alzheimer’s disease (AD). The Ts65Dn (Ts) mouse model recapitulates both cognitive and morphological deficits of DS and AD, including BFCN degeneration. Therefore, this study used Ts mice to understand mechanisms underlying BFCN degeneration to identify novel targets for therapeutic intervention. They performed single population RNA sequencing to examine transcriptomic changes within medial septal nucleus BFCNs. To evaluate this, they used laser capture microdissection to individually isolate immunopositive neurons in Ts and normal disomic (2N) mice at 6 months of age. The dataset contains RNA sequencing and immunohistochemistry data.